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Federal Research Center 
"Krasnoyarsk Science Center of the Siberian
Branch of the Russian Academy of Sciences"

 Федеральный исследовательский центр «Красноярский научный центр Сибирского отделения Российской академии наук»

Federal Research Center 
"Krasnoyarsk Science Center of the Siberian
Branch of the Russian Academy of Sciences"

Krasnoyarsk scientists found a structural difference in the genomes of chloroplasts and bacteria

6 May 2020 г.

Красноярские ученые обнаружили структурное отличие в геномах хлоропластов и бактерий
Scientists at the Federal Research Center KSC SB RAS using bioinformatics methods tested whether the affinity of chloroplasts and cyanobacteria is reflected in the frequency characteristics of their genomes. The internal structure of the chloroplast DNA turned out to be significantly different from the DNA structure of bacteria. Thus, the researchers for the first time demonstrated the fundamental structural difference between these genomes. The results of the research are published in the journal “BMC Bioinformatics”.

The study of nucleotide sequences is the most important task of modern molecular biology and, in particular, that of bioinformatics. Specialists in this field of science consider genomes as sets of repeating symbols and try to find certain patterns in them. Based on such information, one can judge about the evolution of living organisms, find a connection between the structure of the genome and the function of the genome-encoded proteins, and solve many other problems. In some respects, the results of the scientists look more like the work of abstract artists, as they are trying to find out something in common in the seeming chaos of life.

It is believed that chloroplasts, where the photosynthesis occurs, originated from cyanobacteria as a result of their symbiosis with other unicellular organisms a little more than one billion years ago. At the same time, chloroplasts have their own DNA. It can be suggested that if they originated from cyanobacteria, a similarity should be observed not only between the sequence of nucleotides, but also between other gene characteristics of these two biological objects. Using bioinformatics methods, Krasnoyarsk scientists decided to test if the affinity of chloroplasts and cyanobacteria is reflected in such a parameter as the frequency characteristics of their genomes.

Previously, scientists found that using certain algorithms, the bacterial genome can be represented as an almost regular hexagon, where at the vertices and center there are clusters of DNA fragments with the same frequency of occurrence of consecutive nucleotide triplets. As a result of a similar methodology for the analysis of the structure of the chloroplast genome, the Krasnoyarsk scientists discovered another cluster structure. Numerical manipulations with 178 genomes of chloroplasts of various plants show that they are characterized by eight sets of relatively short DNA fragments which are completely formal and have the same triplet distribution.

To see the cluster structure of the genome, the scientists covered each genome with a set of intersecting fragments of the same length. Then, each fragment was transformed into a dictionary of 63 triplets - three consecutive nucleotides. A cluster structure occurs when each triplet dictionary is represented by a point in a 63-dimensional space, where the frequency of triplets plays the role of dimensionality. The projection onto the plane of the distribution of these points in the 63-dimensional space looks different for bacteria and chloroplasts. For chloroplasts, all selected genome fragments are divided into eight classes according to the frequency of triplets.

“Our study shows a huge difference between the structure of the chloroplast genome and bacterial ones. So, we brought into question the hypothesis on the universality of the seven-cluster structure of any genomes. At least for chloroplasts, eight clusters are distinguished in the genome structure. In the future, we are planning to clarify our results by including more plants into the study. In general, such an analysis is useful not only for finding an answer to a rather narrow question on the origin of chloroplasts, but also for solving fundamental problems. For example, we can study the role of “junk” or non-coding nucleotide sequences in the functioning and evolution of genomes, ”emphasizes Mikhail Sadovsky, Doctor of Physical and Mathematical Sciences, leading researcher at the Institute of Computational Modeling KSC SB RAS.